May 2014 - galaxy-dev - lists.galaxyproject.org

new_tool_panel_section_label web api
by Evan Bollig 23 May '14

23 May '14

I am using the new_tool_panel_section_label option when installing tools from the toolshed (via scripts/api/install_tool_shed_repository.py. It works, but I'm curious if its producing the wrong result. See the attached image. I have installed a bunch of tools with new_tool_panel_section_label="Other (Main Tool Shed)". I see in the tool_conf.xml that the tool is installed under a section, and the section name gives the menu option its string (e.g., "Other (Main Tool Shed)"). A <label> on the other hand is contained within a section and gives a subheading string (see expected_section_and_label.png). If the parameter "new_tool_panel_section_label" specifies the section_name, what option exists to specify the label? Or perhaps was the "*_label" option intended to provide the subheading and another option (e.g., new_tool_panel_section_name supposed to exist)? Cheers, -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan(a)msi.umn.edu boll0107(a)umn.edu

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Display problem with partial loading of tabular data
by Peter Cock 23 May '14

23 May '14

Hello all, Large tabular data files in Galaxy are shown with "auto loading", meaning more data is loaded as you scroll down the page. (As an aside, this can cause confusion, e.g. using CTRL+F to search in the web browser would miss not-yet-loaded content.) I've noticed with many BLAST tabular files with 25 columns (often quite wide with sequences in columns 21 and 22) that Galaxy does not load enough to fill the page. e.g. Only 14 rows are shown. I order to get the rest to load (on Firefox or Safari at least), I must scroll *right* to trigger more to load. This is a problem as at first glance the interface implies that the fill dataset is loaded - there is no vertical scroll bar or other visual indicator :( Have I explained this clearly enough? Would some images help? Thanks, Peter

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Repository installation on multiple servers
by Kandalaft, Iyad 23 May '14

23 May '14

Hi Everyone This is my first time on the mailing list. I am the administrator for a production installation of Galaxy at Agriculture and Agri-Food Canada in Ottawa, Canada. Currently, I have a galaxy configured to start 3 web servers and 3 handlers. When installing a tool from a toolshed, only one of the three servers sees the installation (the one that processed the installation request). To resolve the issue, galaxy needs to be restarted, which reloads all the tools. Is this the expected behaviour when a proxy server (apache) load balances 3 galaxy web servers? If not, where can I start diagnosing the problem? Your assistance is much appreciated. Thank you. Regards, Iyad Kandalaft Bioinformatics Programmer Microbial Biodiversity Bioinformatics Science & Technology Branch Agriculture & Agri-Food Canada Iyad.Kandalaft(a)agr.gc.ca | (613) 759-1228

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dynamic number of outputs in workflow context
by Jun Fan 23 May '14

23 May '14

Dear all, I have a tool which generates dynamic number of mzid outputs depending on the number of selected files and tools ( = number of files * number of tools). The suggested methods to deal with this situation are 1) composite html which contains links to all outputs or 2) put output files in the $__new_file_path__ with some naming convention. Neither of these can specify the output type of the tool to the desired value "mzid", which makes it impossible to connect this tool to the downstream tool taking mzid as input. My solution to this is to limit to single file selection, then listing all possible mzid output files with filter elements. I am wondering whether there is better solution to solve this. Another question about workflow: if a tool A can generate two types of output: C and D, and another tool B can take type C, D and E as its input, it is fine to connect these two tools A and B in the workflow. However, if the types selected for input and output do not match (e.g. type C for tool A output and type D for tool B input or even type E), how to configure galaxy to spot this inconsistency? Best regards! Jun

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download workflow error
by Evan Bollig 22 May '14

22 May '14

I have a fresh instance of galaxy-dist#stable. I create users and upload a workflow via the internal python api, and then I attempt to edit and download the workflow from the workflow editor tab. I click the direct download link and get the attached exception. I found that the exception is avoided if I instead share/export the workflow and then create a public username when prompted. When I go back and use the direct download link again, it works. Not sure if they're directly connected, but something in the share/export seems to band-aid the other. Presumably the 'None' should be the public username. Cheers, -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan(a)msi.umn.edu boll0107(a)umn.edu

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Galaxy is not running
by Wally Atterberry 22 May '14

22 May '14

Hi, I am new to Galaxy, so am probably doing something silly. My jobs do not finish and sometimes do not start. Here is the error message: Details user username watterber quota_percent 3 total_disk_usage 10295907343 nice_total_disk_usage 9.6 GB email atterber(a)unlv.nevada.edu is_admin false tags_used model_class User id e2b7da49063484ac source HDACollection(d686c5fd139f68f1,190) xhr readyState 4 responseText {"err_msg": "Uncaught exception in exposed API method:", "err_code": 0} responseJSON err_msg Uncaught exception in exposed API method: err_code 0 status 500 statusText Internal Server Error responseHeaders Server nginx/1.4.7 Date Thu, 22 May 2014 16:23:06 GMT Content-Type application/json Transfer-Encoding chunked Connection keep-alive Cache-Control max-age=0,no-cache,no-store options data parse true emulateHTTP false emulateJSON false Any information would be awesome. Thank you, Wally

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TestToolShed NameError: global name 'suc' is not defined
by Peter Cock 22 May '14

22 May '14

Hi all, I just hit a bug on the TestToolShed, (1) Goto http://testtoolshed.g2.bx.psu.edu/ (2) Login (3) Click "Latest revision: failing tool tests" or similar links (4) Observer error page, NameError: global name 'suc' is not defined This is working on the main ToolShed. Regards, Peter -- Internal Server Error Galaxy was unable to successfully complete your request URL: http://testtoolshed.g2.bx.psu.edu/repository/browse_my_writable_repositorie… Module galaxy.web.framework.middleware.error:149 in __call__ >> app_iter = self.application(environ, sr_checker) Module paste.debug.prints:106 in __call__ >> environ, self.app) Module paste.wsgilib:543 in intercept_output >> app_iter = application(environ, replacement_start_response) Module paste.recursive:84 in __call__ >> return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ >> return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ >> return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request >> body = method( trans, **kwargs ) Module galaxy.webapps.tool_shed.controllers.repository:239 in browse_my_writable_repositories_with_failing_tool_tests >> return self.my_writable_repositories_with_failing_tool_tests_grid( trans, **kwd ) Module galaxy.web.framework.helpers.grids:80 in __call__ >> query = self.build_initial_query( trans, **kwargs ) Module tool_shed.grids.repository_grids:1083 in build_initial_query >> grids_util.filter_by_latest_downloadable_changeset_revision_that_has_failing_tool_tests( trans, repository ) Module tool_shed.grids.util:89 in filter_by_latest_downloadable_changeset_revision_that_has_failing_tool_tests >> repository_metadata = get_latest_downloadable_repository_metadata_if_it_includes_tools( trans, repository ) Module tool_shed.grids.util:196 in get_latest_downloadable_repository_metadata_if_it_includes_tools >> repository_metadata = get_latest_downloadable_repository_metadata( trans, repository ) Module tool_shed.grids.util:180 in get_latest_downloadable_repository_metadata >> latest_downloadable_revision = suc.get_previous_metadata_changeset_revision( repository, repo, tip_ctx, downloadable=True ) NameError: global name 'suc' is not defined extra data full traceback text version This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem.

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warning text
by Evan Bollig 21 May '14

21 May '14

Galaxy Team: I'm confused. This warning appears when I import an old workflow into the latest version of galaxy-dist#stable. As I interpret the first message, I see "galaxy has fastqc 0.3 installed, but the workflow was written with fastqc 0.52 and will need to be updated to use the version 0.3 tool". This must be wrong, no? Perhaps I'm installing tools from the wrong toolshed, but I would expect the main galaxy toolshed to have *newer*, not older versions of tools available as months progress. My guess is that your verbose message needs to be polished. If you look at the second attached screenshot, I believe that confirms that I have fastqc 0.52 installed. In that case, you probably need to tell users, "fastqc: using version '0.52' instead of version '0.3' indicated in this workflow." (note that the version strings are swapped). Perhaps add a bit more to the message to avoid confusion. Cheers, -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan(a)msi.umn.edu boll0107(a)umn.edu

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Fwd: Fwd: genotypeGVCFs in galaxy from GATK 3.0
by florian 21 May '14

21 May '14

Hello, I am working on it; I already integrate some tools of GATK3 in a dedicated instance of galaxy; -> RealignerTargetCreator <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_w…> -> IndelRealigner <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_w…> -> HaplotypeCaller <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_w…> These are the tools that I use most; I have written the wrappers in java ... I need at least one or two more week to achieve a package that could be published in a tool shed (for testing) Florian -------- Message original -------- Sujet: [galaxy-dev] genotypeGVCFs in galaxy from GATK 3.0 Date : Tue, 20 May 2014 17:25:55 -0700 De : Nikhil Joshi <najoshi(a)ucdavis.edu> Pour : galaxy-dev(a)lists.bx.psu.edu <galaxy-dev(a)lists.bx.psu.edu> Hi all, Is anyone working on (or has already created) wrappers for GATK 3.0? Specifically, I'm looking for a wrapper for genotypeGVCFs, but it seems like I would want all the GATK wrappers to be updated. Any help is highly appreciated! - Nik. -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w)

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genotypeGVCFs in galaxy from GATK 3.0
by Nikhil Joshi 21 May '14

21 May '14

Hi all, Is anyone working on (or has already created) wrappers for GATK 3.0? Specifically, I'm looking for a wrapper for genotypeGVCFs, but it seems like I would want all the GATK wrappers to be updated. Any help is highly appreciated! - Nik. -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w)

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